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The flooding is mostly tidal and most likely to happen in November and December, but wind and rain also play a part at any time of year. The greatest chances for any flooding are at the new and full moon phases, neither of which will occur in early October this year. (Full moon Sept. 28th, new moon Oct. 13th.)

There's nothing to be "worried" about. If there is flooding, the water rises for a few hours and then drains away. The most susceptible areas are obviously the low points in the city, and elevated walkways are set up along several 'streets' for pedestrians.

You can take a vaporetto to Burano and Murano and to Torcello, which I think is wonderful, nothing but a great old church and a couple of restaurants, very few inhabitants and numerous cats. Unless you particularly want a tour guide there is no reason you need one for an island visit.

Free rides to Murano seemed to be offered all over sponsored by the bigger factories. This usually includes a demonstration, and then the hard sell.

We went there on our own via the Vaporetto years ago with our kids. I think the stops was 1 stop further then where most of the big factories are (someone else may be able to give better advice as far as where to get off). We walked around the town, had lunch, and asked around where we may find a workshop. We eventually were pointed in the right direction, to a small workshop where the craftsmen were working. There was 1 man who did the little animals (that they sell all over) and 2 others working on an exotic chandelier. It was quite amazing to watch these 2 men in action. We were all mesmerized. It was almost like watching a dance performance, the way they moved around and handled the glass.

Unfortunately I never wrote down the name or location, but it was a bit off the beaten path.

I was never in Venice during the flooding, but have been when the platforms were set up in preparation.

I agree, take the Vaporetto, water bus... after doing some homework of your own on line, and deciding which islands you want to see most, and even research some of the glass makers, etc. Go at your own pace, no hard sell feeling of obligation. Stop for a coffee, or lunch.. no schedule to keep, except to maybe catch the next Vaporetto... Check several departure times on the charts as you get off.
I've been to Venice 4 times, never had the Aqua Alta's, but have seen the ramps up. Only about 4 foot wide, I can't imagine people passing others, or traveling both directions.